Sodium in PDB 5hn3: Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form)

The structure of Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form), PDB code: 5hn3 was solved by T.Shimizu, T.Tomita, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.00 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.102, 91.447, 175.990, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.8

The binding sites of Sodium atom in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form) (pdb code 5hn3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form), PDB code: 5hn3:

Sodium binding site 1 out of 1 in the Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-Decarboxylating Dehydrogenase (TK0280) From Thermococcus Kodakarensis (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:24.7 occ:1.00 O A:HIS250 2.3 22.4 1.0 O A:HOH543 2.3 25.3 1.0 O A:PRO248 2.4 18.9 1.0 O A:HOH597 2.4 36.2 1.0 O A:HOH686 2.5 30.4 1.0 O A:VAL249 2.8 21.1 1.0 C A:VAL249 3.1 21.3 1.0 C A:HIS250 3.2 20.3 1.0 C A:PRO248 3.5 20.8 1.0 CA A:VAL249 3.6 20.9 1.0 N A:HIS250 3.7 19.5 1.0 OE2 A:GLU247 3.8 22.8 1.0 O A:HOH612 3.9 31.3 1.0 O A:HOH522 3.9 36.9 1.0 N A:VAL249 4.0 20.2 1.0 CA A:HIS250 4.0 21.8 1.0 N A:GLY251 4.1 23.4 1.0 CA A:GLY251 4.3 24.1 1.0 O A:GLY67 4.4 24.4 1.0 CD A:GLU247 4.6 22.8 1.0 O A:HOH717 4.6 48.6 1.0 CG A:PRO248 4.7 22.2 1.0 CA A:PRO248 4.7 20.2 1.0 CB A:ALA68 4.8 26.6 1.0 O A:HOH697 4.9 44.0 1.0 N A:PRO248 4.9 21.3 1.0 CG A:GLU247 4.9 22.9 1.0 CB A:PRO248 5.0 21.3 1.0

T.Shimizu, L.Yin, A.Yoshida, Y.Yokooji, S.I.Hachisuka, T.Sato, T.Tomita, H.Nishida, H.Atomi, T.Kuzuyama, M.Nishiyama. Structure and Function of An Ancestral-Type Beta-Decarboxylating Dehydrogenase From Thermococcus Kodakarensis Biochem. J. V. 474 105 2017.
ISSN: ESSN 1470-8728
PubMed: 27831491
DOI: 10.1042/BCJ20160699